Pipeline failure from process 'calling_pipeline:makeReport"

forty2wallabyway commented 2 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

1.3.0

Workflow Execution

Command line (Cluster)

Other workflow execution

In Conda environment

EPI2ME Version

No response

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

This is an issue that seems to occur during a handful of different executions; however, today it occurred after attempting to execute the following:

nextflow run main.nf -profile singularity --bam /lab_data/daniels_lab/tysh/nanopore_seq/calls.bam --out_dir /lab_data/des/ --reference_based_assembly --reference ../references/mycobacteria/NZ_HG964481.1.fasta --override_basecaller_cfg dna_r9.4.1_e8_hac@v3.3

Relevant log output

Caused by:
  Process `calling_pipeline:makeReport` terminated with an error exit status (1)

Command executed:

  workflow-glue report     --stats per_read_stats/*          --prokka               --versions versions     --params params.json     --output wf-bacterial-genomes-report.html     --sample_ids calls

Command exit status:
  1

Command output:
  (empty)

Command error:
  [07:13:01 - workflow_glue] Bootstrapping CLI.
  [07:13:12 - matplotlib] Matplotlib created a temporary cache directory at /tmp/matplotlib-18dbyb0q because the default path (/home/tsherman/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  [07:13:13 - matplotlib.font_manager] generated new fontManager
  [07:13:13 - workflow_glue] Starting entrypoint.
  Traceback (most recent call last):
    File "/home/tsherman/wf-bacterial-genomes/bin/workflow-glue", line 7, in <module>
      cli()
    File "/home/tsherman/wf-bacterial-genomes/bin/workflow_glue/__init__.py", line 82, in cli
      args.func(args)
    File "/home/tsherman/wf-bacterial-genomes/bin/workflow_glue/report.py", line 594, in main
      report = create_report(args, logger)
    File "/home/tsherman/wf-bacterial-genomes/bin/workflow_glue/report.py", line 290, in create_report
      zip(args.sample_ids_with_stats, args.stats), key=lambda x: x[0]
  TypeError: 'NoneType' object is not iterable

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

cjalder commented 2 months ago

Hi @forty2wallabyway thanks for raising this issue. It seems like the workflow isn't finding the per-read-stats file for the sample. How many reads are in the bam file? Do you happen to have the full log you can send to us. Thanks!

forty2wallabyway commented 2 months ago

Thanks for the response @cjalder - there looks to be 698,780 reads in the bam file (checked using samtools).

I attached the nextflow.log: nextflow.log.log

xiranli007 commented 4 weeks ago

hello I have the exact same issue, is it solved?

forty2wallabyway commented 4 weeks ago

Hi @xiranli007, I haven't heard back yet, and haven't been able to resolve the issue, though I did find a workaround by adding the following line into the main.nf under the failing process:

errorStrategy 'ignore'

cjalder commented 1 week ago

Hi guys - could you update the workflow to v1.4.1 and see if the problem persists?

forty2wallabyway commented 1 week ago

Thank you @cjalder - the update resolved the issue for me!

amirh-hajianpour commented 5 days ago

Hello everyone! My problem persists even after updating the workflow to the last version (v1.4.1-gf73d06f). However, I am using FASTQs. Here's my log file: epi2me_bacterial.log

cjalder commented 5 days ago

hi @amirh-hajianpour - looking at your log it seems like the barcodes in the directory and the sample sheet arent matching, meaning no samples are being passed to the workflow.

epi2me-labs / wf-bacterial-genomes